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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTCCCGTGATACACGAGTGGACATACGAGGCCATGTGTCATGATTTATTAAGTCTGGAGGGGAGCAAGTATACATACGAGGTAGATGTACCAAAgttcatggtttatgacactagcgttttttcttttttatagattacaactag

Basic information

species Selaginella moellendorffii
transcript EFJ29221
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29221 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA11G03230.1 (Glycine max), 5'ss of exon 10
ATTGCTCCCGTGATACACGAGTGGACATACGAGGCCATGTGTCATGATTTATTAAGTCTGGAGGGGAGCAAGTATACATACGAGGTAGATGTACCAAAgttcatggtttatg--acactagcgttttttcttttttatagattacaactag------------------
|||||||| |||||||| || ||||| || || |||||||||||||||||  | | | ||||||| |  || |||    | || |||  |    |||  |||     | |      | |   || ||  || | ||||| || |  || |                   
ATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAAgtaacttctacaattttcccttctcactctgaatttttgtgttaactctcttatacataaacacaaaatcttctgtatttttaag

upper sequence: EFJ29221 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA01G42140.1 (Glycine max), 5'ss of exon 6
ATTGCTCCCGTGATACACGAGTGGACATACGAGGCCATGTGTCATGATTTATTAAGTCTGGAGGGGAGCAAGTATACATACGAGGTAGATGTACCAAAgttca--tggtttatgacactagcgttttttcttttttatagattacaactag------------------
|||||||| |||||||| || ||||| || || |||||||||||||||||  | | | ||||||| |  || |||    | || |||  |    |||  |||   ||         | |   || ||  || | ||||| || |  || |                   
ATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAAgtaacttctacaattttcccttgtcactctgaatttttgtgttaactctcttatacataaacacaaaatctactgtatttttaag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169113298|gb|FE515249.1|FE515249
EST:     CATACGAG--A--T-TAC-AACTAG                         CTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
genomic: CATACGAGGTAGATGTACCAA--A-gttcatggtt ... ttacaactagCTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
EST: gi|169113298|gb|FE515249.1|FE515249
EST:     CATACGAG--A--T-TAC-AACTAG                         CTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
genomic: CATACGAGGTAGATGTACCAA--A-gttcatggtt ... ttacaactagCTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
EST: gi|169078646|gb|FE487078.1|FE487078
EST:     CATAC---G-AGAT-TA-CAACTAG                         CTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
genomic: CATACGAGGTAGATGTACCAA--A-gttcatggtt ... ttacaactagCTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
EST: gi|169078646|gb|FE487078.1|FE487078
EST:     CATAC---G-AGAT-TA-CAACTAG                         CTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
genomic: CATACGAGGTAGATGTACCAA--A-gttcatggtt ... ttacaactagCTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
EST: gi|169116012|gb|FE517375.1|FE517375
EST:     CATACGAG--A--T-TAC-AACTAG                         CTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
genomic: CATACGAGGTAGATGTACCAA--A-gttcatggtt ... ttacaactagCTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
EST: gi|169116012|gb|FE517375.1|FE517375
EST:     CATACGAG--A--T-TAC-AACTAG                         CTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA
genomic: CATACGAGGTAGATGTACCAA--A-gttcatggtt ... ttacaactagCTCTGGTAAAAGAGAACAGAAGGAAGTTCTCCTCGAAGAACATGACCCTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCTCCCGTGATACACGAGTGGACATACGAGGCCATGTGTCATGATTTATTAAGTCTGGAGGGGAGCAAGTATACATACGAGGTAGATGTACCAAAgttcatggtttatgacactagcgttttttcttttttatagattacaactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG